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comparison distance.xml @ 6:9fb9fed71486 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
author nml
date Fri, 12 Oct 2018 09:16:03 -0400
parents b69e898b8109
children dcd43b402eb3
comparison
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5:b69e898b8109 6:9fb9fed71486
88 <help><![CDATA[ 88 <help><![CDATA[
89 89
90 Quasispecies Distance 90 Quasispecies Distance
91 ===================== 91 =====================
92 92
93 Determines the evolutionary distance between viral quasispecies. 93 This tool determines the cosine relatedness between viral quasispecies, reporting either angular cosine distance or cosine similarity as measures of relatedness. These measures of relatedness should be understood as approximations for evolutionary distance and might be useful for performing clustering.
94 Uses the angular cosine distance function by default.
95 94
96 ------ 95 ------
97 Inputs 96 Inputs
98 ------ 97 ------
99 98
100 1. FASTA Consensus file 99 1. A reference FASTA.
101 2. Two or more BAM files (otherwise tool will throw an error) 100 2. At least two BAM files generated in coordination with the above reference.
102 101
103 ---------- 102 ----------
104 Parameters 103 Parameters
105 ---------- 104 ----------
106 1. Normalize pileup (True or False) 105
106 1. Normalize pileup (True or False).
107 2. Select custom start and end position. Currently only supports selection of custom start and end position for one single reference. 107 2. Select custom start and end position. Currently only supports selection of custom start and end position for one single reference.
108 3. Choose how to treat zero coverage regions (keep, remove all, or truncate) 108 3. Choose how to treat zero coverage regions (keep, remove all, or truncate).
109 109
110 ------- 110 -------
111 Outputs 111 Outputs
112 ------- 112 -------
113 113
114 CSV containing distance matrix. 114 A CSV file containing a matrix of similarities or distances, as requested by the user.
115 115
116 ]]></help> 116 ]]></help>
117 <citations> 117 <citations>
118 <citation type="bibtex"> 118 <citation type="bibtex">
119 @misc{GitHubquasitoolsdistance, 119 @misc{GitHubquasitoolsdistance,